Basic pixel data types

Most microscopic file formats contain either 8bit or 16bit unsigned pixel data, but there are exceptions. The following table summarizes how the file pixel data is handled in Huygens:

8 bit Image

16 bit Image

32 bit Image

ics

32 bit

ics

16 bit

ics

8 bit

ics2

32 bit

hdf5

32 bit

tiff

16 bit

tiff

8 bit

tiff-rgb

8 bit

lsm

12 bit

lsm

8 bit

pic

16 bit

pic

8 bit

r3d

32 bit

ims

8 bit

ome

32 bit

zvi

16 bit

stk

16 bit

mrc

32 bit

ipl

16 bit

ipm

8 bit

seq

16 bit

lif

16 bit

lif

8 bit

oif

16 bit

nd2

16 bit

Indexed file names

Index suffixes at the end of a filename are interpreted by Huygens as an XY slice or time frame number (depending on the file format). Huygens can read a series of indexed image files contained in a single directory as one 3D of 4D image. Please avoid indexes at the end of filenames that do not stick to the supported conventions. See renaming Tiff series for the supported criteria.

Depending on the file format chosen to save the image the file data type will be 32 bits, 16 bits or 8 bits. The image, as read by Huygens, has either 32 bits, 16 bits or 8 bits as data type. This presents a number of combinations from the data types of the open image to data types of the saved image. This situation is summarized in the following table, where the cells show the data type of the resulting file given a source image and a destination file format:

hdf5

ics

ics2

tiff 8

tiff 16

tiff-rgb

imaris

biorad 8

biorad 16

ome-xml

delta r3d

8 bit Image

8 bit

8 bit

8 bit

8 bit

16 bit

8 bit

8 bit

8 bit

-

8 bit

8 bit

16 bit Image

16 bit

16 bit

16 bit

8 bit

16 bit

8 bit

8 bit

8 bit

16 bit

16 bit

16 bit

32 bit Image

32 bit

32 bit

32 bit

8 bit

16 bit

8 bit

8 bit

8 bit

16 bit

32 bit

32 bit

When the chosen file extension implies fewer bits than those of the image, for example saving a 32 bit image to a 16 bit file, the software will prompt for a conversion method choice: Contrast stretch, Linked stretch or clipping.

Please note that writing to TIFF files may alter the data, see Tiff scaling. JPEG, being a lossy format, i.e. not all the original information is saved, is only intended for visualization purposes and is therefore not listed in the above table.

Metadata import

The software will try to import from the file headers as much information as possible concerning the Microscopic Parameters. This is not always feasible: some formats do not store this information at all, other store it in a way that is difficult to read (see difficulties reading metadata). Huygens made that all directly visible: if you see a green dot all meta data are correct, if you see a blue dot it is nearly correct, with an orange dot there was no information in the metadata at all, Huygens then uses the default ranges for those kind of images. We recommend to check orange and blue values before proceeding with the deconvolution.
If the metadata of a hyperstack image with z stacks of multiple positions is not read by Huygens, it is recommended to save the individual stacks as ics/ids for Huygens.